https://github.com/ChengLiLab/myeloma
Tip revision: 634d6aabda1b3c0bc7ddfe145dfc34b5018b6f63 authored by ChengLiLab on 17 November 2017, 12:16:24 UTC
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Tip revision: 634d6aa
U266_genome_cnv_40kb.R
U266_genome_cnv_40kb <- read.table( file = "/lustre/user/liclab/wupz/DNA_seq/CNV_final/resolution_40kb/U266-merged.sorted.bam.dedup.bam_ratio.txt",
stringsAsFactors = F, header = T, sep = "\t" )
head(U266_genome_cnv_40kb)
U266_cnv_block_40kb <- FindCNVBlock( freec_ratio = U266_genome_cnv_40kb)
head(U266_cnv_block_40kb)
options(digits=14)
U266_cnv_block_40kb_bed <- cbind( chrom = paste( "chr", U266_cnv_block_40kb[, 1],sep = "" ), chromStart = as.integer(U266_cnv_block_40kb[, 2]),
chromEnd = as.integer(U266_cnv_block_40kb[, 2] + 40000), U266_cnv_block_40kb[, 4:6])
write.table(x = U266_cnv_block_40kb_bed, file = "/lustre/user/liclab/wupz/dosageEffect/ngs.plot/U266_cnv_block_40kb.bed",
quote = F, row.names = F, col.names = F, sep = "\t")
U266_cnv_block_40kb[30, 1] == 10
U266_random_sites_40kb <- numeric()
U266_random_TAD_sites_40kb <- numeric()
for ( i in names(table(U266_cnv_block_40kb_bed[, 1]))[1:23] ) {
tmp_length <- sum(U266_cnv_block_40kb_bed[, 1] == i)
# generate a set of random sites used for negative control
tmp_random_bins <- sample(x = sum(U266_all_insulation_bins[, 1] == i), size = tmp_length )
tmp_random_bins_sites <- U266_all_insulation_bins[U266_all_insulation_bins[, 1] == i, ][tmp_random_bins, ]
U266_random_sites_40kb <- rbind( U266_random_sites_40kb, tmp_random_bins_sites)
# generate a set of random TAD sites used for positive control
tmp_random_TAD <- sample(x = sum(U266_all_tad_boundaries[, 1] == i), size = tmp_length )
tmp_random_TAD_sites <- U266_all_tad_boundaries[U266_all_tad_boundaries[, 1] == i, ][tmp_random_TAD, ]
U266_random_TAD_sites_40kb <- rbind(U266_random_TAD_sites_40kb, tmp_random_TAD_sites)
}
head(U266_random_TAD_sites_40kb)
head(U266_random_sites_40kb)
write.table(x = U266_random_TAD_sites_40kb, file = "/lustre/user/liclab/wupz/dosageEffect/ngs.plot/U266_random_TAD_sites_40kb.bed",
quote = F, row.names = F, col.names = F, sep = "\t")
write.table(x = U266_random_sites_40kb, file = "/lustre/user/liclab/wupz/dosageEffect/ngs.plot/U266_random_sites_40kb.bed",
quote = F, row.names = F, col.names = F, sep = "\t" )